The president, accompanied by his wife and several aides, arrived at the Vatican on Wednesday morning and thanked the pope saying it was "a great honour" to be there.
During the meeting, the two leaders with contrasting styles and differing worldviews attempted to broadcast a tone of peace.
The Pope previously denounced policies that didn't welcome migrants. During one of his weekly Wednesday catechism lessons he said: "In the social and civil context as well, I appeal not to create walls but to build bridges.
"To not respond to evil with evil."
Although the pontiff didn't refer to Trump in his comments, it came amid a global uproar over the president's administration's attempts to impose a travel ban on seven mostly Muslim countries.
Returning from a visit last year to the US-Mexico border, he was asked about Trump's campaign pledge to build a border wall and he replied that anyone who wants to build a wall is "not Christian".
In response, Trump said: "For a religious leader to question a person's faith is disgraceful."
The meeting ended 30 minutes later when Francis rang the bell in his private study. Trump's predecessor, Barack Obama, had a private audience with Francis at the Vatican in 2014 that lasted 50 minutes.
The pope gave the president a medal featuring an olive branch, among other gifts prompting Trump to say "We can use peace".
According to NPR, he also gave the president copies of his writings, "Including his encyclical on climate change - a topic on which Trump has a very different opinion".
Austen Ivereigh, UK-based Catholic writer and journalist told Premier's News Hour that the tension at the beginning of the meeting wasn't present by the end.
Ivereigh said: "They were much more relaxed with each other, there were smiles, there was exchanges of gifts - there was clearly some warmth there."
He continued that journalists overheard Trump tell the pope at the end of the meeting "I won't forget what you said", although it's not clear what he was referring to.
Ivereigh added: "That was an important gesture that certainly the meeting had some impact on him."
Trump presented the pontiff some books written by Martin Luther King Jr and said: "I think you'll enjoy them. I hope you do."
After the meeting, Trump met with Italy's Prime Minister Paolo Gentiloni where pool reporters were allowed to visit. When asked about meeting Francis, Trump said: "He is something.
"We had a fantastic meeting."
He has since changed the background of his twitter page to a picture from his meeting with the Pope.
Listen to Austen Ivereigh speaking with Premier's Marcus Jones:
